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MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

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MultiQC is published in Bioinformatics:

MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

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Final Multiqc Report

https://github.com/Daylily-Informatics/daylily (BRANCH:* sentb) (TAG:grape-ape.v1) (HASH:d7edfe2f)

Project/Budget: da-us-west-2d-giab-sownsamp-test
Budget @ Runtime: $0.0 of $200.0 spent ( 0%)
Spot Instances: c6i.32xlarge c7i.48xlarge c7i.metal-48xl m7i.metal-48xl
Spot Costs per hr: median: $2.97 mean: $2.79 ( avg cost per vcpu,per min: $0.000242214 )
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Results Dir (GB): 63G

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Report generated on 2025-05-12, 20:04 UTC based on data in: /fsx/analysis_results/ubuntu/ont_ds/daylily/results/day/hg38

Controls Concordance Report

Concordance Stats For The GIAB HC Regions For This Sample.

Showing ⁰/₂₇ rows and ¹⁹/₁₉ columns.

mqc_id	SNPClass	Sample	TgtRegionSize	TN	FN	TP	FP	Fscore	Sensitivity-Recall	Specificity	FDR	PPV	Precision	AltId	CmpFootprint	AllVarMeanDP	CovBin	Aligner	SNVCaller
Ods5x_HG006_sup-PAY77227_0-ont-sentdont-All	All	Ods5x_HG006_sup-PAY77227_0	2,518,942,743.0	2,515,247,063.0	514,177.0	3,181,503.0	149,628.0	0.9	0.9	1.0	0.0	1.0	1.0	HG006	giabHC	-1.0	-2.0	ont	sentdont
Ods5x_HG006_sup-PAY77227_0-ont-sentdont-DEL_50	DEL_50	Ods5x_HG006_sup-PAY77227_0	2,518,942,743.0	2,518,736,212.0	85,278.0	121,253.0	25,980.0	0.7	0.6	1.0	0.2	0.8	0.8	HG006	giabHC	-1.0	-2.0	ont	sentdont
Ods5x_HG006_sup-PAY77227_0-ont-sentdont-DEL_gt50	DEL_gt50	Ods5x_HG006_sup-PAY77227_0	2,518,942,743.0	2,518,942,742.0	1.0	0.0	12.0		0.0	1.0	1.0	0.0	0.0	HG006	giabHC	-1.0	-2.0	ont	sentdont
Ods5x_HG006_sup-PAY77227_0-ont-sentdont-INS_50	INS_50	Ods5x_HG006_sup-PAY77227_0	2,518,942,743.0	2,518,738,602.0	84,679.0	119,462.0	22,656.0	0.7	0.6	1.0	0.2	0.8	0.8	HG006	giabHC	-1.0	-2.0	ont	sentdont
Ods5x_HG006_sup-PAY77227_0-ont-sentdont-INS_gt50	INS_gt50	Ods5x_HG006_sup-PAY77227_0	2,518,942,743.0	2,518,942,733.0	3.0	7.0	29.0	0.3	0.7	1.0	0.8	0.2	0.2	HG006	giabHC	-1.0	-2.0	ont	sentdont
Ods5x_HG006_sup-PAY77227_0-ont-sentdont-Indel_50	Indel_50	Ods5x_HG006_sup-PAY77227_0	2,518,942,743.0	2,518,923,916.0	9,492.0	9,335.0	826.0	0.6	0.5	1.0	0.1	0.9	0.9	HG006	giabHC	-1.0	-2.0	ont	sentdont
Ods5x_HG006_sup-PAY77227_0-ont-sentdont-Indel_gt50	Indel_gt50	Ods5x_HG006_sup-PAY77227_0	2,518,942,743.0	2,518,942,496.0	62.0	185.0	4.0	0.8	0.7	1.0	0.0	1.0	1.0	HG006	giabHC	-1.0	-2.0	ont	sentdont
Ods5x_HG006_sup-PAY77227_0-ont-sentdont-SNPts	SNPts	Ods5x_HG006_sup-PAY77227_0	2,518,942,743.0	2,516,726,506.0	222,252.0	1,993,985.0	68,832.0	0.9	0.9	1.0	0.0	1.0	1.0	HG006	giabHC	-1.0	-2.0	ont	sentdont
Ods5x_HG006_sup-PAY77227_0-ont-sentdont-SNPtv	SNPtv	Ods5x_HG006_sup-PAY77227_0	2,518,942,743.0	2,517,893,057.0	112,410.0	937,276.0	31,289.0	0.9	0.9	1.0	0.0	1.0	1.0	HG006	giabHC	-1.0	-2.0	ont	sentdont
Ods10x_HG006_sup-PAY77227_0-ont-sentdont-All	All	Ods10x_HG006_sup-PAY77227_0	377,862,616.0	377,419,692.0	24,676.0	418,248.0	104,667.0	0.9	0.9	1.0	0.2	0.8	0.8	HG006	clinvar_genes	-1.0	-2.0	ont	sentdont
Ods10x_HG006_sup-PAY77227_0-ont-sentdont-DEL_50	DEL_50	Ods10x_HG006_sup-PAY77227_0	377,862,616.0	377,837,036.0	6,194.0	19,386.0	16,824.0	0.6	0.8	1.0	0.5	0.5	0.5	HG006	clinvar_genes	-1.0	-2.0	ont	sentdont
Ods10x_HG006_sup-PAY77227_0-ont-sentdont-DEL_gt50	DEL_gt50	Ods10x_HG006_sup-PAY77227_0	377,862,616.0	377,862,610.0	5.0	1.0	65.0	0.0	0.2	1.0	1.0	0.0	0.0	HG006	clinvar_genes	-1.0	-2.0	ont	sentdont
Ods10x_HG006_sup-PAY77227_0-ont-sentdont-INS_50	INS_50	Ods10x_HG006_sup-PAY77227_0	377,862,616.0	377,837,055.0	6,441.0	19,120.0	13,025.0	0.7	0.7	1.0	0.4	0.6	0.6	HG006	clinvar_genes	-1.0	-2.0	ont	sentdont
Ods10x_HG006_sup-PAY77227_0-ont-sentdont-INS_gt50	INS_gt50	Ods10x_HG006_sup-PAY77227_0	377,862,616.0	377,862,606.0	6.0	4.0	283.0	0.0	0.4	1.0	1.0	0.0	0.0	HG006	clinvar_genes	-1.0	-2.0	ont	sentdont
Ods10x_HG006_sup-PAY77227_0-ont-sentdont-Indel_50	Indel_50	Ods10x_HG006_sup-PAY77227_0	377,862,616.0	377,860,146.0	781.0	1,689.0	2,198.0	0.5	0.7	1.0	0.6	0.4	0.4	HG006	clinvar_genes	-1.0	-2.0	ont	sentdont
Ods10x_HG006_sup-PAY77227_0-ont-sentdont-Indel_gt50	Indel_gt50	Ods10x_HG006_sup-PAY77227_0	377,862,616.0	377,862,533.0	14.0	69.0	196.0	0.4	0.8	1.0	0.7	0.3	0.3	HG006	clinvar_genes	-1.0	-2.0	ont	sentdont
Ods10x_HG006_sup-PAY77227_0-ont-sentdont-SNPts	SNPts	Ods10x_HG006_sup-PAY77227_0	377,862,616.0	377,594,796.0	7,475.0	260,345.0	45,243.0	0.9	1.0	1.0	0.1	0.9	0.9	HG006	clinvar_genes	-1.0	-2.0	ont	sentdont
Ods10x_HG006_sup-PAY77227_0-ont-sentdont-SNPtv	SNPtv	Ods10x_HG006_sup-PAY77227_0	377,862,616.0	377,741,222.0	3,760.0	117,634.0	26,833.0	0.9	1.0	1.0	0.2	0.8	0.8	HG006	clinvar_genes	-1.0	-2.0	ont	sentdont
Ods15x_HG006_sup-PAY77227_0-ont-sentdont-All	All	Ods15x_HG006_sup-PAY77227_0	3,088,286,401.0	3,084,448,522.0	125,165.0	3,712,714.0	1,315,480.0	0.8	1.0	1.0	0.3	0.7	0.7	HG006	hg38	-1.0	-2.0	ont	sentdont
Ods15x_HG006_sup-PAY77227_0-ont-sentdont-DEL_50	DEL_50	Ods15x_HG006_sup-PAY77227_0	3,088,286,401.0	3,088,066,552.0	42,089.0	177,760.0	172,301.0	0.6	0.8	1.0	0.5	0.5	0.5	HG006	hg38	-1.0	-2.0	ont	sentdont
Ods15x_HG006_sup-PAY77227_0-ont-sentdont-DEL_gt50	DEL_gt50	Ods15x_HG006_sup-PAY77227_0	3,088,286,401.0	3,088,286,362.0	37.0	2.0	583.0	0.0	0.1	1.0	1.0	0.0	0.0	HG006	hg38	-1.0	-2.0	ont	sentdont
Ods15x_HG006_sup-PAY77227_0-ont-sentdont-INS_50	INS_50	Ods15x_HG006_sup-PAY77227_0	3,088,286,401.0	3,088,066,564.0	45,613.0	174,224.0	135,131.0	0.7	0.8	1.0	0.4	0.6	0.6	HG006	hg38	-1.0	-2.0	ont	sentdont
Ods15x_HG006_sup-PAY77227_0-ont-sentdont-INS_gt50	INS_gt50	Ods15x_HG006_sup-PAY77227_0	3,088,286,401.0	3,088,286,359.0	26.0	16.0	2,497.0	0.0	0.4	1.0	1.0	0.0	0.0	HG006	hg38	-1.0	-2.0	ont	sentdont
Ods15x_HG006_sup-PAY77227_0-ont-sentdont-Indel_50	Indel_50	Ods15x_HG006_sup-PAY77227_0	3,088,286,401.0	3,088,256,363.0	6,482.0	23,556.0	32,680.0	0.5	0.8	1.0	0.6	0.4	0.4	HG006	hg38	-1.0	-2.0	ont	sentdont
Ods15x_HG006_sup-PAY77227_0-ont-sentdont-Indel_gt50	Indel_gt50	Ods15x_HG006_sup-PAY77227_0	3,088,286,401.0	3,088,285,364.0	95.0	942.0	2,199.0	0.5	0.9	1.0	0.7	0.3	0.3	HG006	hg38	-1.0	-2.0	ont	sentdont
Ods15x_HG006_sup-PAY77227_0-ont-sentdont-SNPts	SNPts	Ods15x_HG006_sup-PAY77227_0	3,088,286,401.0	3,086,002,285.0	19,938.0	2,264,178.0	514,709.0	0.9	1.0	1.0	0.2	0.8	0.8	HG006	hg38	-1.0	-2.0	ont	sentdont
Ods15x_HG006_sup-PAY77227_0-ont-sentdont-SNPtv	SNPtv	Ods15x_HG006_sup-PAY77227_0	3,088,286,401.0	3,087,203,480.0	10,885.0	1,072,036.0	455,380.0	0.8	1.0	1.0	0.3	0.7	0.7	HG006	hg38	-1.0	-2.0	ont	sentdont

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: giab_concordance-plot_table

Sort	Column	Description	ID
\|\|	SNPClass	SNPClass	`SNPClass`
\|\|	Sample	Sample	`Sample`
\|\|	TgtRegionSize	TgtRegionSize	`TgtRegionSize`
\|\|	TN	TN	`TN`
\|\|	FN	FN	`FN`
\|\|	TP	TP	`TP`
\|\|	FP	FP	`FP`
\|\|	Fscore	Fscore	`Fscore`
\|\|	Sensitivity-Recall	Sensitivity-Recall	`Sensitivity_Recall`
\|\|	Specificity	Specificity	`Specificity`
\|\|	FDR	FDR	`FDR`
\|\|	PPV	PPV	`PPV`
\|\|	Precision	Precision	`Precision`
\|\|	AltId	AltId	`AltId`
\|\|	CmpFootprint	CmpFootprint	`CmpFootprint`
\|\|	AllVarMeanDP	AllVarMeanDP	`AllVarMeanDP`
\|\|	CovBin	CovBin	`CovBin`
\|\|	Aligner	Aligner	`Aligner`
\|\|	SNVCaller	SNVCaller	`SNVCaller`

Rules Benchmark Data2

Showing ⁰/₁₂ rows and ²³/₂₃ columns.

combined_rule	sample	rule	s	h:m:s	max_rss	max_vms	max_uss	max_pss	io_in	io_out	mean_load	cpu_time	hostname	ip	nproc	cpu_efficiency	instance_type	region_az	spot_cost	snakemake_threads	task_cost	rule_prefix	rule_suffix
ont.sentdont.1-24-Ods5x_HG006_sup-PAY77227_0.	Ods5x_HG006_sup-PAY77227_0.	ont.sentdont.1-24	3,990.5	1:06:30	38,996.0	50,226.1	38,969.0	38,972.8	19,382.1	13,408.2	18,343.8	672,821.9	i192-dy-all-3	10.0.1.102	192.0	168.6	c7i.48xlarge	us-west-2d	3.0	192.0	3.3	ont	sentdont.1-24
ont.sentdont.1-24-Ods10x_HG006_sup-PAY77227_0.	Ods10x_HG006_sup-PAY77227_0.	ont.sentdont.1-24	2,391.1	0:39:51	39,000.3	50,223.1	39,087.4	39,092.8	26,761.6	7,476.2	17,611.7	364,350.0	i192-dy-all-1	10.0.1.76	192.0	152.4	c7i.48xlarge	us-west-2d	3.0	192.0	2.0	ont	sentdont.1-24
ont.sentdont.1-24-Ods15x_HG006_sup-PAY77227_0.	Ods15x_HG006_sup-PAY77227_0.	ont.sentdont.1-24	1,710.6	0:28:30	38,990.1	50,223.1	38,997.2	39,002.4	32,709.4	4,349.7	16,070.1	230,807.8	i192-dy-all-4	10.0.1.145	192.0	134.9	c7i.48xlarge	us-west-2d	3.0	192.0	1.4	ont	sentdont.1-24
ont.sentdont.concat.fofn-Ods5x_HG006_sup-PAY77227_0.	Ods5x_HG006_sup-PAY77227_0.	ont.sentdont.concat.fofn	0.4	0:00:00	3.2	7.7	0.1	0.3	0.0	0.0	0.0	0.0	ip-10-0-0-216	52.11.194.193	8.0	0.0	r7i.2xlarge	us-west-2d	0.2	1.0	0.0	ont	sentdont.concat.fofn
ont.sentdont.concat.fofn-Ods10x_HG006_sup-PAY77227_0.	Ods10x_HG006_sup-PAY77227_0.	ont.sentdont.concat.fofn	0.4	0:00:00	15.3	38.7	6.4	6.8	0.0	0.0	0.0	0.0	ip-10-0-0-216	52.11.194.193	8.0	0.0	r7i.2xlarge	us-west-2d	0.2	1.0	0.0	ont	sentdont.concat.fofn
ont.sentdont.concat.fofn-Ods15x_HG006_sup-PAY77227_0.	Ods15x_HG006_sup-PAY77227_0.	ont.sentdont.concat.fofn	0.4	0:00:00	3.2	7.7	0.1	0.3	0.0	0.0	0.0	0.0	ip-10-0-0-216	52.11.194.193	8.0	0.0	r7i.2xlarge	us-west-2d	0.2	1.0	0.0	ont	sentdont.concat.fofn
ont.sentdont.concordance-Ods5x_HG006_sup-PAY77227_0.	Ods5x_HG006_sup-PAY77227_0.	ont.sentdont.concordance	2,729.4	0:45:29	60,118.7	364,649.9	60,156.0	60,157.3	1,360.3	12,594.3	116.7	567.7	i192-dy-all-1	10.0.1.73	192.0	0.2	c7i.metal-48xl	us-west-2d	2.6	96.0	1.0	ont	sentdont.concordance
ont.sentdont.concordance-Ods10x_HG006_sup-PAY77227_0.	Ods10x_HG006_sup-PAY77227_0.	ont.sentdont.concordance	2,698.8	0:44:58	90,369.3	359,201.0	90,422.0	90,423.1	3,226.6	11,518.6	128.6	549.0	i192-dy-all-4	10.0.1.145	192.0	0.2	c7i.48xlarge	us-west-2d	3.0	96.0	1.1	ont	sentdont.concordance
ont.sentdont.concordance-Ods15x_HG006_sup-PAY77227_0.	Ods15x_HG006_sup-PAY77227_0.	ont.sentdont.concordance	2,512.4	0:41:52	102,426.2	359,201.0	102,467.8	102,468.9	3,079.7	10,998.7	126.7	616.7	i192-dy-all-4	10.0.1.145	192.0	0.2	c7i.48xlarge	us-west-2d	3.0	96.0	1.0	ont	sentdont.concordance
ont.sentdont.merge-Ods5x_HG006_sup-PAY77227_0.	Ods5x_HG006_sup-PAY77227_0.	ont.sentdont.merge	67.1	0:01:07	79.1	13,418.8	82.4	82.8	0.0	494.7	142.8	103.2	i192-dy-all-1	10.0.1.73	192.0	1.5	c7i.metal-48xl	us-west-2d	2.6	64.0	0.0	ont	sentdont.merge
ont.sentdont.merge-Ods10x_HG006_sup-PAY77227_0.	Ods10x_HG006_sup-PAY77227_0.	ont.sentdont.merge	41.9	0:00:41	78.9	12,139.0	82.2	82.7	6.0	201.5	84.5	39.3	i192-dy-all-9	10.0.1.108	192.0	0.9	c7i.metal-48xl	us-west-2d	2.6	64.0	0.0	ont	sentdont.merge
ont.sentdont.merge-Ods15x_HG006_sup-PAY77227_0.	Ods15x_HG006_sup-PAY77227_0.	ont.sentdont.merge	30.7	0:00:30	78.8	12,523.0	83.2	83.4	6.0	238.4	144.6	46.2	i192-dy-all-4	10.0.1.145	192.0	1.5	c7i.48xlarge	us-west-2d	3.0	64.0	0.0	ont	sentdont.merge

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: rules_benchmark_data2-section-plot_table

Sort	Column	Description	ID
\|\|	sample	sample	`sample`
\|\|	rule	rule	`rule`
\|\|	s	s	`s`
\|\|	h:m:s	h:m:s	`h_m_s`
\|\|	max_rss	max_rss	`max_rss`
\|\|	max_vms	max_vms	`max_vms`
\|\|	max_uss	max_uss	`max_uss`
\|\|	max_pss	max_pss	`max_pss`
\|\|	io_in	io_in	`io_in`
\|\|	io_out	io_out	`io_out`
\|\|	mean_load	mean_load	`mean_load`
\|\|	cpu_time	cpu_time	`cpu_time`
\|\|	hostname	hostname	`hostname`
\|\|	ip	ip	`ip`
\|\|	nproc	nproc	`nproc`
\|\|	cpu_efficiency	cpu_efficiency	`cpu_efficiency`
\|\|	instance_type	instance_type	`instance_type`
\|\|	region_az	region_az	`region_az`
\|\|	spot_cost	spot_cost	`spot_cost`
\|\|	snakemake_threads	snakemake_threads	`snakemake_threads`
\|\|	task_cost	task_cost	`task_cost`
\|\|	rule_prefix	rule_prefix	`rule_prefix`
\|\|	rule_suffix	rule_suffix	`rule_suffix`

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